The Japanese I've spoken to don't know the answer either LOL. According to an unofficial, casual survey I've conducted with my students past and present, Japanese ranks way up among the subjects they hate the most. LOL
As for the counting system, my guess is that they copied and modified the counting system from China, as the Chinese use a similar counting system.
I'm contemplating doing articles on the various counting systems, but I'm still trying to think of a way to present them as clearly and easily-understandable as possible.